No abstract

The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies. The new entry format provides a greater flexibility, simplifies maintenance and allows the capture of more information from the literature. The new disorder ontology has been formalized and made interoperable by adopting the OWL format, as well as its structure and term definitions have been improved. The new annotation interface has made the curation process faster and more effective. We recently showed that new DisProt annotations can be effectively used to train and validate disorder predictors. We believe the growth of DisProt will accelerate, contributing to the improvement of function and disorder predictors and therefore to illuminate the ‘dark’ proteome.

The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure.

-nitrosylation, a prototypic redox-based posttranslational modification, is frequently dysregulated in disease. -nitrosoglutathione reductase (GSNOR) regulates protein-nitrosylation by functioning as a protein denitrosylase. Deficiency of GSNOR results in tumorigenesis and disrupts cellular homeostasis broadly, including metabolic, cardiovascular, and immune function. Here, we demonstrate that GSNOR expression decreases in primary cells undergoing senescence, as well as in mice and humans during their life span. In stark contrast, exceptionally long-lived individuals maintain GSNOR levels. We also show that GSNOR deficiency promotes mitochondrial nitrosative stress, including excessive -nitrosylation of Drp1 and Parkin, thereby impairing mitochondrial dynamics and mitophagy. Our findings implicate GSNOR in mammalian longevity, suggest a molecular link between protein-nitrosylation and mitochondria quality control in aging, and provide a redox-based perspective on aging with direct therapeutic implications.

S-nitrosoglutathione reductase (GSNOR) represents the bestdocumented denitrosylase implicated in regulating the levels of proteins posttranslationally modified by nitric oxide on cysteine residues by S-nitrosylation. GSNOR controls a diverse array of physiologic functions, including cellular growth and differentiation, inflammation, and metabolism. Chromosomal deletion of GSNOR results in pathologic protein S-nitrosylation that is implicated in human hepatocellular carcinoma (HCC). Here we identify a metabolic hallmark of aberrant S-nitrosylation in HCC and exploit it for therapeutic gain. We find that hepatocyte GSNOR deficiency is characterized by mitochondrial alteration and by marked increases in succinate dehydrogenase (SDH) levels and activity. We find that this depends on the selective S-nitrosylation of Cys 501 in the mitochondrial chaperone TRAP1, which mediates its degradation. As a result, GSNORdeficient cells and tumors are highly sensitive to SDH inhibition, namely to a-tocopheryl succinate, an SDH-targeting molecule that induced RIP1/PARP1-mediated necroptosis and inhibited tumor growth. Our work provides a specific molecular signature of aberrant S-nitrosylation in HCC, a novel molecular target in SDH, and a first-in-class therapy to treat the disease. Cancer Res; 76(14); 4170-82. Ó2016 AACR.

the whole E13,5 brain and in the olfactory bulbs (OB) of E18,5 brain (Fig. 1b, Extended Data Fig. 1d, e). Also, neural stem cells (NSCs) isolated from Ambra1 cKO mice show increased levels of several cell-cycle regulatory proteins (Fig. 1c, Extended Data Fig. 1f, g), together with higher clonogenic potential and replication rate (Fig 1d, Extended Data Fig. 1h). Strikingly, levels of cyclin D1 and D2 proteins and phosphorylated pRb (S807/811) are highly increased both ex and in vivo (Fig. 1c, e, Extended Data Fig. 1g, i-m), suggesting an AMBRA1dependent Cyclin D modulation. Indeed, consistent with our previous results 7 , we find in neural ex vivo and in vitro cell lines that AMBRA1 directly binds and regulates the stability of N-Myc, via the phosphatase PP2A, thereby controlling Cyclin D1 and D2 transcription (Extended Data Fig. 1n-r). Moreover, we noticed that both cyclin D1 and D2 are highly resilient to proteasomal degradation in Ambra1-deficiency conditions (Fig. 1f, Extended Data Fig. 2a, b). In line with the fact that both Myc and D-type cyclins positively regulate G1/S transition 10,11 , Ambra1 cKO NSCs show a shorter G1 phase with faster entry into, and longer residence in S phase (Extended Data Fig. 2c). By reducing cyclin D/CDK kinase activity we could restore proliferation to wt levels (Extended Data Fig. 2d), highlighting the importance of accelerated G1/S transition in the AMBRA1depleted driven phenotype. Additionally, we found that due to Ambra1 deficiency, deregulated cell cycle progression is followed by increased cell death, a phenotype rescued upon cyclin D/CDK activity inhibition (Extended Data Fig. 2e, f). Of note, Ambra1 deficiency in neurodevelopment promotes staminal niche

The centrosome is the master orchestrator of mitotic spindle formation and chromosome segregation in animal cells. Centrosome abnormalities are frequently observed in cancer, but little is known of their origin and about pathways affecting centrosome homeostasis. Here we show that autophagy preserves centrosome organization and stability through selective turnover of centriolar satellite components, a process we termed doryphagy. Autophagy targets the satellite organizer PCM1 by interacting with GABARAPs via a C-terminal LIR motif. Accordingly, autophagy deficiency results in accumulation of large abnormal centriolar satellites and a resultant dysregulation of centrosome composition. These alterations have critical impact on centrosome stability and lead to mitotic centrosome fragmentation and unbalanced chromosome segregation. Our findings identify doryphagy as an important centrosome-regulating pathway and bring mechanistic insights to the link between autophagy dysfunction and chromosomal instability. In addition, we highlight the vital role of centriolar satellites in maintaining centrosome integrity.

No abstract